Based on high-resolution analysis to a 280-cm long sediment core obtained from the muddy area in the central Yellow Sea, we examined the provenance of muddy sediments and discussed the changing marine sedimentary environment since the middle Holocene. The results indicated that fine-grained sediments in the muddy area were mainly derived from the Huanghe (Yellow River) and Changjiang (Yangtze River) with considerable stepwise variations during the past 6.6 kyr. The Yellow Sea Warm Current was initiated at 6 kyr when the sea level was high together with the enhanced East Asian Winter Monsoon. These in combination established the framework of shelf circulation in the Yellow Sea that began to trap the river-derived fine-grained sediments. From 4.9 kyr to 2.8 kyr, both the Kushiro Current and East Asian Monsoon were significantly weakened, reducing the delivery of Changjiang sediments to the muddy area. As a result, the sediments were mainly originated from the Huanghe. From 2.8 kyr to 1.5 kyr the continuously weakened East Asian Winter Monsoon and enhanced Yellow Sea Warm Current entrapped more fine-grain sediments. Whereas the enhanced East Asian Winter Monsoon and the human caused increase in sediment load of the Huanghe since 1.5 kyr, and direct delivery of Huanghe sediments to the Yellow Sea during 1128–1855 AD might dominated the sedimentation in the study area. The stepwise variations of the sediment provenance and composition of the Central Yellow Sea muddy sediments are of importance to understanding the formation of muddy deposit in the central Yellow Sea and the associated variations of marine environment since the middle Holocene.